DeepH-pack
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mzjb
failure when i run the process
it processed the error.log [stdout of cmd "/data/home/scv7f2x/run/julia-1.6.6/bin/julia /data/home/scv7f2x/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl --input_dir /data/run01/scv7f2x/software-scv7f2x/DeepH-pack/example/work_dir/dataset/raw/0 --output_dir /data/run01/scv7f2x/software-scv7f2x/DeepH-pack/example/work_dir/dataset/processed/0 --save_overlap false"]:
[stderr of cmd "/data/home/scv7f2x/run/julia-1.6.6/bin/julia /data/home/scv7f2x/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl --input_dir /data/run01/scv7f2x/software-scv7f2x/DeepH-pack/example/work_dir/dataset/raw/0 --output_dir /data/run01/scv7f2x/software-scv7f2x/DeepH-pack/example/work_dir/dataset/processed/0 --save_overlap false"]:
ERROR: LoadError: AssertionError: DeepH-pack only supports OpenMX v3.9. Please check your OpenMX version Stacktrace: [1] parse_openmx(filepath::String; return_DM::Bool) @ Main ~/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl:160 [2] get_data(filepath_scfout::String, Rcut::Float64; if_DM::Bool) @ Main ~/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl:321 [3] top-level scope @ ~/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl:424 in expression starting at /data/home/scv7f2x/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl:424
i'm sure that i installed the openmx3.9 ,so i don't know to slove it
the raw file is included output openmx.cif openmx.out openmx.scfout openmx.std openmx.xyz openmx_in.dat poscar
how to solve it thanks
How did you confirm that you were using openmx v3.9?
You can use the command head /data/run01/scv7f2x/software-scv7f2x/DeepH-pack/example/work_dir/dataset/raw/0/openmx.out to check the version.
it can be see that i use the openmx v3.9
/data/run01/scv7f2x/software-scv7f2x/DeepH-pack/example/work_dir/dataset/raw/0/openmx.out
This calculation was performed by OpenMX Ver. 3.9 using 64 MPI processes and 1 OpenMP threads.
Thu Mar 28 14:45:26 2024
System.Name openmx DATA.PATH /data/home/scv7f2x/run/software-scv7f2x/openmx3.9/DFT_DATA19 HS.fileout on
Species.Number 1 <Definition.of.Atomic.Species Bi Bi8.0-s3p2d2 Bi_PBE19 Definition.of.Atomic.Species> Atoms.Number 36 Atoms.SpeciesAndCoordinates.Unit FRAC .....
it also can be see
[stdout of cmd "/data/home/scv7f2x/run/julia-1.6.6/bin/julia /data/home/scv7f2x/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl --input_dir /data/run01/scv7f2x/software-scv7f2x/DeepH-pack/example/work_dir/dataset/raw/167 --output_dir /data/run01/scv7f2x/software-scv7f2x/DeepH-pack/example/work_dir/dataset/processed/167 --save_overlap false"]:
[stderr of cmd "/data/home/scv7f2x/run/julia-1.6.6/bin/julia /data/home/scv7f2x/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl --input_dir /data/run01/scv7f2x/software-scv7f2x/DeepH-pack/example/work_dir/dataset/raw/167 --output_dir /data/run01/scv7f2x/software-scv7f2x/DeepH-pack/example/work_dir/dataset/processed/167 --save_overlap false"]:
ERROR: LoadError: AssertionError: DeepH-pack only supports OpenMX v3.9. Please check your OpenMX version Stacktrace: [1] parse_openmx(filepath::String; return_DM::Bool) @ Main ~/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl:160 [2] get_data(filepath_scfout::String, Rcut::Float64; if_DM::Bool) @ Main ~/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl:321 [3] top-level scope @ ~/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl:424 in expression starting at /data/home/scv7f2x/.conda/envs/dl/lib/python3.9/site-packages/deeph/preprocess/openmx_get_data.jl:424
You can upload the files openmx.out, openmx.scfout, openmx.std, and openmx_in.dat here, and we'll take a look at what's going on.
thanks ,because the format of the file ,we have sent the files to your mail "He Li" [email protected]